Presentation

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ARTbio works with the Galaxy system, a collaborative open source platform dedicated to scientific and biomedical research. The Galaxy servers enable computational data analyses with a user-friendly interface. They provide both reproducibility and transparency of the analyses which can be shared for collaboration and publication.

Our Services

  • We assist you in the experimental and computational design of high-throughput sequencing analyses using Galaxy servers.
  • We help you choose the tools and workflow best adapted to your analyses.
  • We provide advanced training in Galaxy usage.
  • Our services are fully accessible to both public and private structures. Please contact us for pricing.

Our Expertise

  • We have an extensive knowledge of the Galaxy software and its use, from raw data acquisition to publication.
  • We constantly integrate newly launched software and methods into the Galaxy framework and build workflows for complex computational treatments.
  • We ensure project quality and optimal interaction with users by using continuous integration technologies and the AGILE guidelines.
  • We continuously improve our Galaxy expertise through our own research in RNA biology, epigenetics, metagenomics and bioinformatics, which we publish in peer reviewed scientific journals.

Our Technology

  • We use the R, Python, Perl and Bash programming languages, the Git and Mercurial revision control software, and continuous integration tools such as Planemo and Jenkins.
  • We implement virtualization and container technologies (e.g. Docker) in order to make analyses reproducible in any hardware infrastructure.
  • We can increase our computing resources on demand thanks to cloud infrastructures such as that provided by the Institut Français de Bioinformatique.

Developments

Project Support

We have recently provided advanced support to many Next Generation Sequencing (NGS) projects, including studies of epigenetic functions of piRNAs [1], antiviral RNA interference [2] or roles of miRNAs in stem cell differentiation [3].

Tools

We developed and made publicly available the « mississippi » suite of tools (for mi, si and pi RNA) for mining small RNA sequencing datasets [4]. We are currently releasing a set of Galaxy workflows aimed at detecting viruses or identifying new viral species from small RNA sequencing datasets [5]. We are also developing the DockerToolFactory, which allows execution of customized R, python, perl or bash scripts without leaving the Galaxy environment [6].

Methodology Developments

We are working to provide solution for continuous integration of tools & workflows in Galaxy server instance(e.g. Planemo, Jenkins CI), automatic deployment of servers in local or cloud environment (e.g. Ansible, Puppet, Virtualization and Docker containers), and transparency & preservation of computational analyses (e.g. regeneration by workflow, iRODS).

  1. A. de Vanssay et al., Paramutation in Drosophila linked to emergence of a piRNA-producing locus. Nature. 490, 112-15 (2012).
  2. P. Miesen et al., Distinct sets of PIWI proteins produce arbovirus and transposon-derived piRNAs in Aedes aegypti mosquito cells. Nucleic Acids Res. (2015), doi:10.1093/nar/gkv590.
  3. A. Jouneau et al., Naive and primed murine pluripotent stem cells have distinct miRNA expression profiles. RNA. 18, 253-64 (2012).
  4. https://testtoolshed.g2.bx.psu.edu/view/mvdbeek/mississippi_toolsuite/
  5. https://toolshed.g2.bx.psu.edu/view/drosofff/suite_visitor2/
  6. https://bitbucket.org/mvdbeek/dockertoolfactory